rs2072744

Positions:

• chrX-43740189-T-C

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_000240.4(MAOA):​c.1107-492T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.54 (12263 hom., 17508 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: MAOA NM_000240.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0680

Genes affected

MAOA (HGNC:6833): (monoamine oxidase A) This gene is one of two neighboring gene family members that encode mitochondrial enzymes which catalyze the oxidative deamination of amines, such as dopamine, norepinephrine, and serotonin. Mutation of this gene results in Brunner syndrome. This gene has also been associated with a variety of other psychiatric disorders, including antisocial behavior. Alternatively spliced transcript variants encoding multiple isoforms have been observed. [provided by RefSeq, Jul 2012]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAOA	NM_000240.4	c.1107-492T>C		intron_variant		ENST00000338702.4
MAOA	NM_001270458.2	c.708-492T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAOA	ENST00000338702.4	c.1107-492T>C		intron_variant		1	NM_000240.4	P1

Frequencies

GnomAD3 genomes AF: 0.537 AC: 59506 AN: 110736 Hom.: 12274 Cov.: 23 AF XY: 0.530 AC XY: 17495 AN XY: 32998

Gnomad AFR AF: 0.307

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.627

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.631

Gnomad NFE AF: 0.659

Gnomad OTH AF: 0.557

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.537 AC: 59502 AN: 110786 Hom.: 12263 Cov.: 23 AF XY: 0.530 AC XY: 17508 AN XY: 33058

Gnomad4 AFR AF: 0.307

Gnomad4 AMR AF: 0.622

Gnomad4 ASJ AF: 0.627

Gnomad4 EAS AF: 0.425

Gnomad4 SAS AF: 0.356

Gnomad4 FIN AF: 0.592

Gnomad4 NFE AF: 0.659

Gnomad4 OTH AF: 0.556

Alfa AF: 0.591 Hom.: 4511

Bravo AF: 0.531

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.4
DANN	Benign	0.85

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2072744; hg19: chrX-43599436;